Re: [galaxy-user] Troubles with Bowtie alignement of sRNA dataset (against precursor of mirBase)

Hi people, I have a litle problem with Bowtie alignments. I am tryin to align sRNA Illumina dataset to hairpin mirbase. The problem is that after the steps (detailed below) I only obtain reads of 15-18nt, and I know that I have a lot of microRNAs (20-22nt) in my data. Beside the size problem, I realized that when the reads and the reference (the precursor in any case) the sequences don't match as I would expect. The sequential steps that I've made: - Groom - Clip (adaptor elimination) - Bowtie against hairpin database (mirBase precursor) - SAM-to-BAM - Download Bam and Bai files - Open in IGV the file and the hairpin database May be I am doing something really bad, but I dont know. Any help/suggestion/tip? Thanks in advance ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/